8I64

Crystal structure of Mycobacterium tuberculosis Uracil-DNA glycosylase in complex with Barbituric acid, Form II


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WRU 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH8.52930.1 M Tris pH 8.5, 25% (w/v) PEG 3350
Crystal Properties
Matthews coefficientSolvent content
1.9938.26

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 69.07α = 90
b = 44.42β = 98.34
c = 67.76γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 345 mm plate2020-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODEBRUKER AXS MICROSTAR1.54179

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.2625.9699.760.0850.9875.8629672
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.262.3410.36560.774

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4WRU2.2625.97916050199.80.19470.191280.25592RANDOM23.844
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
3.6-2.54-1.81-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.301
r_dihedral_angle_4_deg18.8
r_dihedral_angle_3_deg17.544
r_dihedral_angle_1_deg7.047
r_long_range_B_refined4.82
r_long_range_B_other4.771
r_mcangle_it2.621
r_mcangle_other2.62
r_scangle_other2.598
r_angle_other_deg2.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.301
r_dihedral_angle_4_deg18.8
r_dihedral_angle_3_deg17.544
r_dihedral_angle_1_deg7.047
r_long_range_B_refined4.82
r_long_range_B_other4.771
r_mcangle_it2.621
r_mcangle_other2.62
r_scangle_other2.598
r_angle_other_deg2.314
r_mcbond_other1.639
r_mcbond_it1.638
r_scbond_it1.592
r_scbond_other1.591
r_angle_refined_deg1.58
r_chiral_restr0.064
r_bond_other_d0.034
r_gen_planes_other0.009
r_bond_refined_d0.007
r_gen_planes_refined0.007
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1708
Nucleic Acid Atoms
Solvent Atoms129
Heterogen Atoms13

Software

Software
Software NamePurpose
REFMACrefinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing